Image Analysis Software for Computational Morphodynamics
Image Analysis Suites/Database Systems (Free tools)
- BISQUE - "software platform for visualizing, manipulating, and understanding Life Science and bio-medical data coming from all types of sources and modalities."
- Open Microscopy Environment (OME) - deconvolution, visualization, analysis
Commercial Packages (some include limited free/trialware versions)
- amira - "software platform for visualizing, manipulating, and understanding Life Science and bio-medical data coming from all types of sources and modalities."
- Huygens - deconvolution, visualization, analysis
- IDL – Data Visualization Solutions - "data analysis, visualization, and application development"
- ImagePro - 2D and 3D image processing, enhancement, and analysis software with extensive measurement and customization features
- Imaris - visualization, tracking, filament tracing.
- Kitware - ActiVIz, VolView, MIDAS (also open source VTK)
- Mayachitra imago - store, organize, manipulate scientific images like a photo browser (freeware demo version).
- MetaMorph - ".. image acquisition, processing, and analysis.."
- Mimics - 3D Medical Imaging, Visualization
- Zeiss Software - includes AxioVision, Deconvolution, 3D Reconstruction, LSM Image Browser (free version)
Free/Open Source/Shareware Packages
- AIDA - Adaptive Image Deconvolution Algorithm
- Bsoft - Bsoft is a collection of programs and a platform for development of software for image and molecular processing in structural biology.
- DINO - real-time 3D visualization program for structural biology data.
- FAIR - Matlab files for Flexible Image Registration algorithm.
- GoFigure / Digital Fish (kitware version)
- ImageJ - ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh.
- Image SXM - (Mac) Image SXM is a version of the public domain image analysis software NIH Image that has been extended to handle the loading, display and analysis of scanning microscope images. Image SXM supports SAM, SCM, SEM, SFM, SLM, SNOM, SPM and STM image
- IMOD - a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections.
- ITK - NLM Insight segmentation and registration toolkit.
- MESA-3D - Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.
- microManager - Open Source software package for imaging and control of automated microscopes on multiple platforms (Windows, Mac and Linux).
- netpbm - toolbox for manipulation of graphics images including conversion between different formats.
- NIH Image - NIH Image is a public domain image processing and analysis program for the Macintosh.
- OpenDX - a package for the visualization of scientific, engineering and analytical data
- OsiriX - DICOM and other formats (LSM,BioRadPIC, TIff, ANALYZE, PNG, JPG, PDF, QT, AVI, MPG, MPG4) viewer for Macs.
- ParaView (Parallel Visualization Application) ParaView is an open-source, multi-platform application designed to visualize data sets of size varying from small to very large.
- POV-RAY - The Persistence of Vision Ray-Tracer creates three-dimensional, photo-realistic images using a rendering technique called ray-tracing. It reads in a text file containing information describing the objects and lighting in a scene and generates an image of that scene from the view point of a camera also described in the text file.
- PRIISM/IVE - a collection of tools for processing, analyzing, and visualizing multidimensional imagery with a focus on 3D wide-field optical microscopy and EM tomography.
- 3DSlicer - a multi-platform, free open source software (FOSS) for visualization and image computing. The platform provides functionality for segmentation, registration and three-dimensional visualization of multi-modal image data, as well as advanced image analysis algorithms for diffusion tensor imaging, functional magnetic resonance imaging and image-guided therapy. Standard image file formats are supported, and the application integrates interface capabilities to biomedical research software and image informatics frameworks.
- SPIDER - SPIDER (System for Processing Image Data from Electron microscopy and Related fields) is an image processing system for electron microscopy.
- VTK (Kitware)
- Xmipp - "X-Window-based Microscopy Image Processing Package", (J. Struct. Biol. 148, 194-204) is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy.
Review Papers and Tutorials
Peng, H. "Bioimage informatics: a new area of engineering biology", Bioinformatics. 24(17):1827-1836.
Kerlopian AR et al, "A review of imaging techniques for systems biology." BMC Systems Biology 2:74 (2008)
Eils R and Chaitanya A. "Computational imaging in cell biology." Journal of Cell Biology. 161(3):477-481 (2003)
Meijering E and van Cappellen G. "Biological Image Analysis Primer" (2006). (Tutorial). Erasmus Medical Center. Rotterdam, Netherlands.
